Code

Longread only functionality#718

Code

Open

muabnezor wants to merge 35 commits intonf-core:devnf-core/mag:devfrom muabnezor:longread_onlymuabnezor/mag:longread_onlyCopy head branch name to clipboard

+5,174-205

Commits

Commits on Nov 25, 2024

• Add longread only test config

  muabnezor

  committed
  5ffb327

  Copy full SHA for 5ffb327

• Change samplesheet validation schema to allow for longread-only samplesheets

  muabnezor

  committed
  695da2b

  Copy full SHA for 695da2b

• Check if both short, and long reads are given

  muabnezor

  committed
  f67b6b3

  Copy full SHA for f67b6b3

• fix validation schema for samplesheet

  muabnezor

  committed
  bb78aab

  Copy full SHA for bb78aab

Commits on Nov 26, 2024

• Merge remote-tracking branch 'upstream/dev' into longread_only

  muabnezor

  committed
  992b01e

  Copy full SHA for 992b01e

• Add separate wubworkflow for longread host removal

  muabnezor

  committed
  bfd404c

  Copy full SHA for bfd404c

• Add longread meta-assemblers metaflye and metamdbg

  muabnezor

  committed
  387284d

  Copy full SHA for 387284d

• Add longread assemble config

  muabnezor

  committed
  6948316

  Copy full SHA for 6948316

Commits on Nov 27, 2024

• Prepare binning for longread assemblies

  muabnezor

  committed
  762f12b

  Copy full SHA for 762f12b

Commits on Nov 28, 2024

• Fix config and how long reads are prepared for binning

  muabnezor

  committed
  c7a5cdf

  Copy full SHA for c7a5cdf

• change jgi_summarize_bam_contig_depths --percentidentity default from 97 to 90 when dealing with longreads

  muabnezor

  committed
  18ae00d

  Copy full SHA for 18ae00d

• Fix longread binning preparation from all combination of assemblies, and reads

  muabnezor

  committed
  8a22939

  Copy full SHA for 8a22939

Commits on Nov 29, 2024

• format

  muabnezor

  committed
  038a87b

  Copy full SHA for 038a87b

• Fix longread hostremoval, and fix --longread_percentidentiy parameter in config

  muabnezor

  committed
  3ff8de2

  Copy full SHA for 3ff8de2

• Add test_longread to profiles, and ci testing

  muabnezor

  committed
  e277290

  Copy full SHA for e277290

• Fix validation schema, and fix assembly channels for longread and shortread assemblers, when assembly input is given

  muabnezor

  committed
  75a36f2

  Copy full SHA for 75a36f2

• Change logic in samplesheet validation, ch_raw_short_reads should be empty if no files are given

  muabnezor

  committed
  67d44d0

  Copy full SHA for 67d44d0

• fix custom samtools view module

  muabnezor

  committed
  ca4d101

  Copy full SHA for ca4d101

Commits on Dec 5, 2024

• Merge branch 'dev' into longread_only

  muabnezor

  authored
  cfd43e7

  Copy full SHA for cfd43e7

Commits on Dec 6, 2024

• Make sure filtlong works without short reads. the join operator should also return remainder in case the ch_short_reads channel is empty. Change config for FILTLONG to only use '--trim' option if s…

  Show description for 6765ab1
  muabnezor

  committed
  6765ab1

  Copy full SHA for 6765ab1

• Make sure FILTLONG is not run when there are no long reads

  muabnezor

  committed
  e73975c

  Copy full SHA for e73975c

Commits on Dec 11, 2024

• Fix grouping logic for channels in longreads_binning_preparation subworkflow

  muabnezor

  committed
  686fafe

  Copy full SHA for 686fafe

Commits on Dec 12, 2024

• make assembly into subworkflow

  muabnezor

  committed
  a0279fe

  Copy full SHA for a0279fe

• Fix long read assembly input

  muabnezor

  committed
  28f72af

  Copy full SHA for 28f72af

• Update docs

  muabnezor

  committed
  1c4b364

  Copy full SHA for 1c4b364

• Update citations for tools

  muabnezor

  committed
  34067db

  Copy full SHA for 34067db

Commits on Dec 13, 2024

• Fix versions channel in subworkflows

  muabnezor

  committed
  26a0fe7

  Copy full SHA for 26a0fe7

Commits on Jan 7, 2025

• Fix bug when running with --keep_phix, make ch_phix_db_file empty Channel

  muabnezor

  committed
  d9564da

  Copy full SHA for d9564da

• Merge branch 'dev' into longread_only

  muabnezor

  authored
  9087f2f

  Copy full SHA for 9087f2f

• fix modules.config

  muabnezor

  committed
  ba0f831

  Copy full SHA for ba0f831

• Fix linting

  muabnezor

  committed
  d46aa6d

  Copy full SHA for d46aa6d

Commits on Jan 9, 2025

• Use nf-core official module for samtools fastq

  muabnezor

  committed
  f90e5f5

  Copy full SHA for f90e5f5

• Change modules config

  muabnezor

  committed
  85c2e82

  Copy full SHA for 85c2e82

Commits on Jan 10, 2025

• change hybrid logic

  muabnezor

  committed
  7398ba3

  Copy full SHA for 7398ba3

• fix samplesheet validation

  muabnezor

  committed
  ae1953d

  Copy full SHA for ae1953d